Tetramorium are generally polygynous so it's perfectly fine to have multiple queens together, in fact, this generally increases the chances of success for that colony. I'm not sure what you mean by knowing which eggs are fertile and which aren't, when queens are grouped the queens that lay the eggs are often the most dominant ones and any of the queens that do lay eggs are 100% fertile. If they aren't fertile they leave the laying of eggs to the fertile queens because there would be no reason to lay infertile eggs as they would just be eaten by the other queens. Another thing that often happens is any infertile queens will most likely be killed by the other queens, either right off the bat or down the line when workers appear so there is no reason to worry or seperate the queens whatsoever as they will handle that type of thing themselves.
Now as far as when the workers appear, different things can happen. The first is that the workers or other queens will start killing off the submissive queens, either all of them until the most dominant queen remains or leaving any number of queens alive. The other thing that can happen is none of the queens are killed and they all live, there's nothing you can really do to influence what happens but regardless of whatever happens you will likely get a fast growing successful colony out of this. I'd recommend not separating them and the eggs as there is no good way to do this without stressing the queens out which will likely cause them to eat the eggs or die (probably both) and the odds of having even one successful colony out of that will decrease significantly.
